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The Plant Genome : Just Published

 

Accepted, edited articles are published here after author proofing to provide rapid publication and better access to the newest research. Articles are compiled into issues at dl.sciencesocieties.org/publications/tpg, which includes the complete archive.

Citation | Articles posted here are considered published and may be cited by the doi.

Joseph, B., J.A. Schlueter, J.Du, M.A. Graham, J. Ma, and R.C. Shoemaker. 2009. Retrotransposons within Syntenic Regions between Soybean and Medicago truncatula and Their Contribution to Local Genome Evolution. Plant Genome doi:10.3835/plantgenome2009.01.0001

Current issue: Plant Genome 10(2)



  • ORIGINAL RESEARCH

    • Kebede T. Muleta, Peter Bulli, Zhiwu Zhang, Xianming Chen and Michael Pumphrey
      Unlocking Diversity in Germplasm Collections via Genomic Selection: A Case Study Based on Quantitative Adult Plant Resistance to Stripe Rust in Spring Wheat

      Harnessing diversity from germplasm collections is more feasible today because of the development of lower-cost and higher-throughput genotyping methods. However, the cost of phenotyping is still generally high, so efficient methods of sampling and exploiting useful diversity are needed. Genomic selection (GS) has the potential to enhance the use of desirable genetic variation in germplasm collections through predicting the genomic estimated breeding values (GEBVs) for all traits that have been measured. Here, we evaluated the effects of various scenarios of population genetic properties and marker density on the accuracy of GEBVs in the context of applying GS for wheat (Triticum aestivum L.) germplasm use. (continued)

      Core Ideas:
      • Larger germplasm collections may be efficiently sampled via lower-density genotyping methods.
      • The selection population needs to be well represented in the training set.
      • Good prospects for applying genomic selection to efficiently unlock the potential of plant genetic resources exist.

      doi:10.3835/plantgenome2016.12.0124
      Published: August 10, 2017



    • Birgit Samans, Boulos Chalhoub and Rod J. Snowdon
      Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus

      Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of Brassica napus L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. (continued)

      Core Ideas:
      • Homeologous chromosome exchanges drive postpolyploidization genetic diversification in Brassica napus.
      • Homeologous exchanges cause rapid genome size reduction after allopolyploidization.
      • Segmental deletions contain genes associated with adaptive processes and chromosome stability.
      • Breakpoints of genomic rearrangements contain motifs associated with meiotic recombination.
      • Genes involved in chromosome mismatch repair are subject to selection after polyploidization.

      doi:10.3835/plantgenome2017.02.0013
      Published: August 10, 2017



    • Sarah R. Braun, Jeffrey B. Endelman, Kathleen G. Haynes and Shelley H. Jansky
      Quantitative Trait Loci for Resistance to Common Scab and Cold-Induced Sweetening in Diploid Potato

      The development of germplasm with resistance to common scab and cold-induced sweetening is a high priority for the potato (Solanum tuberosum L.) industry. A mapping population was developed from mating two individuals of a diploid family generated by crossing the susceptible cultivated potato clone US-W4 to the highly resistant wild relative (Solanum chacoense Bitter) clone ‘524–8’. Progeny were evaluated in replicated field trials. Tubers were scored for percentage of surface area with scab lesions, scab lesion type, cold-induced sweetening, average tuber weight, and dry matter. (continued)

      Core Ideas:
      • Resistance to common scab and cold-induced sweetening is important to the potato industry.
      • A quantitative trait locus (QTL) for resistance to common scab was identified on chromosome 11.
      • Two QTLs for resistance to cold-induced sweetening were identified on chromosomes 4 and 6.
      • Additional QTLs were detected for vine maturity and tuber weight.
      • This is the first step in the development of molecular markers for use by breeders.

      doi:10.3835/plantgenome2016.10.0110
      Published: August 10, 2017



    • Samar O. Rabah, Chaehee Lee, Nahid H. Hajrah, Rania M. Makki, Hesham F. Alharby, Alawiah M. Alhebshi, Jamal S.M. Sabir, Robert K. Jansen and Tracey A. Ruhlman
      Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew

      In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative rpl22 in cinnamon (Cinnamomum verum J. (continued)

      Core Ideas:
      • DNA sequence data provides valuable information for biotechnology and evolutionary studies.
      • Plastid genomes (plastomes) of 10 nonmodel crop species were sequenced.
      • Inversions, gene divergence and loss, and IR boundary variation were identified.
      • Transfer of mitochondrial DNA to the plastome was found in Anacardium (cashew).

      doi:10.3835/plantgenome2017.03.0020
      Published: August 3, 2017



    • Ismail Y. Rabbi, Lovina I. Udoh, Marnin Wolfe, Elizabeth Y. Parkes, Melaku A. Gedil, Alfred Dixon, Punna Ramu, Jean-Luc Jannink and Peter Kulakow
      Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content

      Cassava is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Primary selection objectives in cassava breeding include dry matter content and micronutrient density, particularly provitamin A carotenoids. These traits are negatively correlated in the African germplasm. This study aimed at identifying genetic markers associated with these traits and uncovering whether linkage and/or pleiotropy were responsible for observed negative correlation. (continued)

      Core Ideas:
      • Cassava, a starchy root crop, is a major source of dietary calories in the tropics.
      • Most varieties consumed are poor in micronutrients, including pro-vitamin A.
      • Dry matter and carotenoid content are governed by few major loci on chromosome 1.
      • Genetic linkage, rather than pleiotropy, is the most likely cause of their negative correlation.

      doi:10.3835/plantgenome2016.09.0094
      Published: August 3, 2017



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